How we work

Step-by-step interdisciplinary guidance for researchers, clinicians and other scientists in order to establish the relevance of sample set data

The description of microbiota is perhaps the most signicant breakthrough in modern medicine. Thanks to the revolution in gene sequencing technology one can now generate large amounts of data from samples of gut microbiota. But generating data is one thing, interpreting and analysing it, in harmony with your clinical study, is quite another. The Microbiota Center Amsterdam is at the forefront of this field and sets itself apart from commercially-oriented “sample testing shops” by providing scientists with multidisciplinary consultancy and study guidance. MiCA’s team includes microbiologists, medical biologists, bioinformaticians and clinicians to help you from study set-up through analysis to interpretation and conclusions.

1. Intake

Pre-test discussion of your study and its parameters

2. Data

Generating sample data and principal component analysis

3. Interpretation

Bioinformatic extraction of the correct information

4. Report

A tailor-made report based on our findings

1. Intake

This is your first official contact with the multidisciplinary team at Microbiota Center Amsterdam (MiCA) — is a personal dialogue aimed at gaining insight into how your study is (or could be) set up, and how microbiota research may help you with the results.

Tailor-made

The intake session takes place with either a microbiologist or a molecular biologist. It is a question and answer session aimed at mutual understanding. This dialogue comprises your study requirements, hypothesis and expectations and MiCA’s insights into the potential role of microbiota and certain testing requirements to enable satisfactory results.

2. Data

Once the intake procedure has been finalized, you will receive an email containing a registration document and instructions on how to provide samples. It is important that you spend time to read the instructions, as the very specific protocols ensure the most reliable final results. You then return the sample information to us and the details are entered into the MiCA database.

Digital DNA

DNA is then isolated from the wet sample and measured for quality. The DNA segments are then amplified. For bacterial profiling the 16S rRNA gene is targeted while for fungal profiling the intergenic transcribe spacers (ITS) are used.

3. Interpretation

While it has been common practice to generate operational taxonomic units (OTU) by clustering the obtained sequences at some set dissimilarity criteria, recent advances in data processing have given us the opportunity to infer the true amplicon sequence variants (ASV). This state-of-the-art bioinformatic data analysis allows for discrimination of variants at single nucleotide level, allowing for the best phylogenetic resolution for further microbiota analysis.

Bioinformatics

Once the ASVs have been inferred, MiCA’s bioinformatics experts interpret that data. The level of interpretation can go from basic analysis (such as alpha diversity and beta diversity), to deeper investigation if, for example, there is other metadata to correlate with the sample data such as patient data, blood samples, diet and BMI. These are not standard procedures and involve close collaboration.

4. Report

The final data output of this part of your diagnostic journey depends on your earlier consultations with the team. The data will be presented in such a way that it fits in with your study set-up, and requirements.

Case-by-case

Each report is generated on a case-by-case basis and is tailor-made according to the mutually agreed sample analysis procedure.